3DFATMIC is a 3-Dimensional Subsurface Flow and Fate and Transport of MIcrobes and Chemicals model. 3DFATMICis designed to simulate transient and/or steady-state density-dependent flow field and transient and/or steady-state distribution of a substrate, a nutrient, an aerobic electron acceptor (e.g., the oxygen), an anaerobic electron acceptor (e.g., the nitrate), and three types of microbes in a three-dimensional domain of subsurface media. 3DFATMIC can handle:

Heterogeneous and anisotropic media consisting of as many geologic formations as desired.

Fate and transport of chemicals ranging from one to seven components.

Employ hexahedral elements, triangular prism, tetrahedral elements, or the mixtures of these three types of elements to facilitate the discretization of the region of interest.

Easy modification of chemical and microbe kinetics.

Both spatially-distributed and point sources/sinks that are spatially- and temporally-dependent.

The prescribed initial conditions by input or by simulating a steady-state version of the system under consideration.

The prescribed transient concentration over Dirichlet nodes.

Time-dependent fluxes over Neumann nodes.

Time-dependent total fluxes over Cauchy nodes.

Variable boundary conditions of evaporation, infiltration, or seepage on the soil-air interface for the flow module and variable boundary conditions of inflow and outflow for the transport module automatically.

Two options of treating the mass matrix - consistent and lumping.

Three options (exact relaxation, under- and over-relaxation) for estimating the nonlinear matrix.

Two options - the Galerkin weighting or upstream weighting for advection term in the transport module.

Two options for the Lagrangian numerical scheme in the transport module which enable and disable the adapted zooming scheme.

Two options for solving the Eulerian step including the enabling and disabling of diffusion zooming.

Mass balance checking over the entire region for every time step.

Modification of the program if different conditions are used.

Scope: 3DFATMIC computes and predicts the distribution of pressure head, moisture content, flow velocity, and total head over a three-dimensional region in either completely saturated, or completely unsaturated, or partially unsaturated or partially saturated subsurface media. It also computes and predicts the spatial-temporal distribution of microbes and multi-chemical components. The media may consist of as many types of soils and geologic units as desired with different material properties. Each soil type may be isotropic or anisotropic. The processes governing the distribution of chemical and microbe concentration and temperature include: (1) reversible sorption, (2) microbe-chemical interaction, and (3) hydrological transport by flow advection/convection, dispersion/diffusion, and effect of unsaturation.

Method: The generalized Richards' equation and Darcy's law governing pressure distribution and water flow in saturated-unsaturated media are simulated with the Galerkin finite-element method subject to appropriate initial and four types of boundary conditions. The equations (a set of PDEs) of transport and fate of chemicals and microbes are derived based on the principle of conservation of mass and the hypothesis of Monod kinetics. The coupled set of PDEs simulated with either the conventional finite-element methods or the hybrid Lagrangian-Eulerian finite-element method with the adaptive local grid refinement and peak capturing scheme subject to appropriate initial and four types of boundary conditions. Hexahedral elements, triangular prism, and tetrahedral elements are used to facilitate the discretization of the region of interest.

Input:(1) Geometry in terms of nodes and elements, and boundaries in terms of nodes and segments; (2) soil properties including (a) saturated hydraulic conductivities or permeabilities; (b) compressibility of water and the media, respectively; (c) bulk density; (d) three soil characteristic curves for each type of soil or geologic unit which are the retention curve, relative conductivity vs. head curve, and water capacity curve; (e) effective porosity; and (f) dispersivities, and effective molecular diffusion coefficient for each soil type or geologic unit; (3) initial distribution of pressure head over the region of interest; (4) net precipitation, allowed ponding depth, potential evaporation, and allowed minimum pressure head in the soil; (5) prescribed pressure head on Dirichlet boundaries; (6) prescribed fluxes of chemicals and heat on Cauchy and/or Neumann boundaries; (7) artificial withdrawals or injections of water; (8) number of chemical components as well as microbes and microbe-chemical interaction parameters such as specific yields, utilization coefficients, saturation constants, etc.; (9) artificial source/sink of water and all chemical components, heat and microbes; (10) prescribed concentrations of all chemical components and microbes as well as temperature on Dirichlet boundaries; (11) prescribed fluxes of all chemical components and heat on variable boundaries; and (12) initial distribution of all chemical component and microbe concentrations and temperature. All inputs in items 4 through 11 can be time-dependent or constant with time.

Output:(1) pressure head, total head, moisture content, and flow velocity over two-dimensional grid at any desired time; (2) water fluxes through all types of boundaries and amount of water accumulated in the media at any desired time; (3) distribution of chemical concentrations, microbes, and temperature over a three-dimensional grid at any desired time; and (4) amount of chemical and heat fluxes through all boundary segments.